By the way, Palaeontologia Electronicarejected the paper that became Why sauropods had long necks; and why giraffes have short necks for what I felt at the time were spurious reasons. (Come to think of it, with the benefit of hindsight and the objectivity of distance, I still think they were spurious reasons.) So that’s why I’m not currently planning to waste my time there again.

BTW., Palaeontologia Electronica, that paper has so far racked up 5,000 unique visitors over on PeerJ. So I’m not unhappy about how it all turned out.

For what it’s worth, my take is that the improvement from the version submitted to PE to the one published in PeerJ is pretty insubstantial — small enough to be outweighed by the cost of the delay in publication.

To be clear, I am not saying that PeerJ’s round of review had no value: anyone can see for themselves that it did. What I’m saying is that the time that extra round took, and the effort that it cost Matt and me — not to mention you, the anonymous reviewer and John — was probably not worth that much improvement. All of us could have more fruitfully spent that time doing new work.

I read from your post on the rejection by PE the quote: “The manuscript reads as a long “story” instead of a scientific manuscript. Material and methods, results, and interpretation are unfortunately not clearly separated.”
Bad mistake, indeed.

Do you mean a bad mistake by the authors or by the reviewers? We wrote it the way we did, by design, because that’s the structure that best conveys the information. Arbitrary adherence to a structure designed to communicate quite different kinds of studies would have been just as worthless as forcing the narrative flow into sonnet structure.

I fully agree with your point of view: “that’s the structure that best conveys the information”. The best thing in this kind of discussions is to present all evidence, as you did, so the reader can make it’s own opinion. I made mine, for example. That quote says more about the bias of the reviewer than about the contents of the article, because it states that such a mean to deliver knowledge is not a “scientific manuscript”. Why not? As long as the story contains all the scientific evidence, this should be praised instead of being criticized, or so I believe.